def test1(self):
"""align two random configurations"""
x0 = _utils.random_configuration(3 * self.natoms)
x1 = _utils.random_configuration(3 * self.natoms)
# subtract center of mass
com = self.measure.get_com(x0)
self.policy.translate(x0, -com)
com = self.measure.get_com(x1)
self.policy.translate(x1, -com)
self.basic_test(x0, x1)
def test1(self):
"""align two random configurations"""
x0 = _utils.random_configuration(3 * self.natoms)
x1 = _utils.random_configuration(3 * self.natoms)
# subtract center of mass
com = self.measure.get_com(x0)
self.policy.translate(x0, -com)
com = self.measure.get_com(x1)
self.policy.translate(x1, -com)
self.basic_test(x0, x1)
def exact_match_test(self, f):
x0 = utils.random_configuration(3 * self.natoms)
x1 = x0.copy()
# apply transformations to x1
f(x1)
self.basic_test(x0, x1)
self.assertLess(self.measure.get_dist(x0, x1), 1e-3)
def exact_match_test(self, f):
x0 = utils.random_configuration(3 * self.natoms)
x1 = x0.copy()
# apply transformations to x1
f(x1)
self.basic_test(x0, x1)
self.assertLess(self.measure.get_dist(x0, x1), 1e-3)
def test2(self):
"""align two configurations that should match exactly
"""
x0 = _utils.random_configuration(3 * self.natoms)
x1 = x0.copy()
self.policy.permute(x1, _utils.random_permutation_permlist(self.permlist, self.natoms))
self.basic_test(x0, x1)
self.assertLess(np.abs(x0-x1).max(), 1e-3)
def test2(self):
"""align two configurations that should match exactly
"""
x0 = _utils.random_configuration(3 * self.natoms)
x1 = x0.copy()
self.policy.permute(
x1, _utils.random_permutation_permlist(self.permlist, self.natoms))
self.basic_test(x0, x1)
self.assertLess(np.abs(x0 - x1).max(), 1e-3)
def test2(self):
"""align two configurations that should match exactly
"""
x0 = _utils.random_configuration(3 * self.natoms)
com = self.measure.get_com(x0)
self.policy.translate(x0, -com)
x1 = x0.copy()
self.policy.rotate(x1, _utils.random_rotation())
self.basic_test(x0, x1)
self.assertLess(np.abs(x0 - x1).max(), 1e-3)
def test2(self):
"""align two configurations that should match exactly
"""
x0 = _utils.random_configuration(3 * self.natoms)
com = self.measure.get_com(x0)
self.policy.translate(x0, -com)
x1 = x0.copy()
self.policy.rotate(x1, _utils.random_rotation())
self.basic_test(x0, x1)
self.assertLess(np.abs(x0-x1).max(), 1e-3)
def apply_tests(self, f):
"""test that that a transofrmation object can reproduce the transformation in f"""
x = _utils.random_configuration(self.natoms * 3)
tform = TransformCluster3D(nsites=self.natoms)
xbkup = x.copy()
x2 = x.copy()
# do transormation
f(tform, x)
tform.apply(x2)
# x2 and x should be the same
self.assertLess(np.abs(x - x2).max(), 1e-3)
def apply_tests(self, f):
"""test that that a transofrmation object can reproduce the transformation in f"""
x = _utils.random_configuration(self.natoms * 3)
tform = TransformCluster3D(nsites=self.natoms)
xbkup = x.copy()
x2 = x.copy()
# do transormation
f(tform, x)
tform.apply(x2)
#x2 and x should be the same
self.assertLess(np.abs(x - x2).max(), 1e-3)
def test1(self):
"""align two random configurations"""
x0 = utils.random_configuration(3 * self.natoms)
x1 = utils.random_configuration(3 * self.natoms)
self.basic_test(x0, x1)
def test1(self):
x0 = _utils.random_configuration(self.natoms * 3)
x1 = _utils.random_configuration(self.natoms * 3)
self.basic_test(x0, x1)
def setUp(self):
self.natoms = 4
self.x1 = _utils.random_configuration(self.natoms * 3).reshape(-1, 3)
self.x2 = _utils.random_configuration(self.natoms * 3).reshape(-1, 3)
def setUp(self):
self.natoms = 11
self.tform = TransformCluster3D()
self.x = _utils.random_configuration(self.natoms * 3)
self.x2 = self.x.copy()
def setUp(self):
self.natoms = 11
self.tform = TransformCluster3D()
self.x = _utils.random_configuration(self.natoms * 3)
self.x2 = self.x.copy()
def test1(self):
x0 = _utils.random_configuration(self.natoms * 3)
x1 = _utils.random_configuration(self.natoms * 3)
self.basic_test(x0, x1)
def setUp(self):
self.natoms = 4
self.x1 = _utils.random_configuration(self.natoms * 3).reshape(-1, 3)
self.x2 = _utils.random_configuration(self.natoms * 3).reshape(-1, 3)
def test1(self):
"""align two random configurations"""
x0 = utils.random_configuration(3 * self.natoms)
x1 = utils.random_configuration(3 * self.natoms)
self.basic_test(x0, x1)
